Differences

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--- hickory [2007/12/13 09:45] – heidi
+++ hickory [2008/07/22 13:31] (current) – external edit 127.0.0.1
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 ====== HICKORY ======
-**[[http://darwin.eeb.uconn.edu/hickory/hickory.html|HICKORY]]**
+{{hickory2.png?400}}\\
+**[[http://darwin.eeb.uconn.edu/hickory/hickory.html|HICKORY]]**\\
+[[http://darwin.eeb.uconn.edu/hickory/documentation/Hickory.pdf|documentation]]
 \\
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   * Windows
   * Linux
 ===== Data type handled =====
   * dominant markers
   * co-dominant markers
+  * AFLP (amplified fragment length polymorphism)
+  * RAPD (random amplified polymorphic DNA)
+  * multi-allelic markers
 ===== Input Files =====
-files in [[NEXUS]] format.
+files in [[NEXUS]] format
-  * need only an alleles block
+  * need only an **alleles block:** <code>
+#nexus
+begin alleles; [comments are surrounded by square brackets]
+ dimensions newpops npops=2 nloci=3;
+ format labels missing=? separator=/;
+ locusallelelabels
+’pgi 1’,
+’pgi 2’,
+adh;
+ matrix
+  Embudo:
+   indiv_1 A/A 100/110 slow/fast
+   indiv_2 A/A 75 / 90 slow/slow
+   indiv_3 A/a 75/100 fast/slow
+   indiv_4 A/A 100/100 fast/fast,
+  Black_Mesa:
+a/a 110/100 fast/slow
+a/A 75/100 slow/slow
+a/a 100/100 fast/fast
+  ;
+end;
+</code>
+    * **dimensions command:**
+      * nloci: number of loci scored
+      * npops: number of populations scored
+    * **format command:**
+      * missing: character to be used for missing data (missing diploid genotype would thus be specified as ?/?)
+    * **locusallelelabels command:**
+      * optional (loci will simply be numbered)
+      * comma-separated list of locus number and locus name pairs
+    * **matrix command:**
+      * The genotype for a diploid locus at a co-dominant locus takes the form A/a
+      * forward slash (/) symbol serves as a separator symbol, making it clear which pairs of alleles belong to each locus
+      * If the loci represent dominant genetic markers, do not use the slash and specify only one allele for each locus
+      * phenotype for a dominant locus (dominant marker):
+        * keyword ''dominant''
+        * dominant phenotype is scored as ''1'' (or ''+'') or ''0'' (''−'') (default)
+        * Hickory accepts the following alternatives: <code>
+dominant;                 -> default
+dominant all:1;           -> default
+dominant all:0;           -> dominant phenotype at all loci scored as 0 (recessive = 1)
+dominant 1,2,3:1 4,5:0;   -> dominant phenotype at first 3 loci scored as 1 and at last 2 loci scored as 0
+dominant 1-3:1 4-5:0;     -> dominant phenotype at first 3 loci scored as 1 and at last 2 loci scored as 0
+</code>
+\\
+  * the **hickory block** is optional:
+    * you can set parameters governing the MCMC sampler
 ===== How to cite =====
+  * Holsinger, K. E. 1999. Analysis of genetic diversity in geographically structured populations: a Bayesian perspective. Hereditas 130:245-255.
+  * Holsinger, K. E., P. O. Lewis, and D. K. Dey. 2002. A Bayesian approach to inferring population structure from dominant markers. Molecular Ecology 11:1157-1164.
+  * Holsinger, K. E., and L. E. Wallace. 2004. Bayesian approaches for the analysis of population structure: an example from Platanthera leucophaea (Orchidaceae). Molecular Ecology 13:887-894.
+  * Song, S., D. K. Dey, and K. E. Holsinger. 2006. Differentiation among populations with migration, mutation, and drift: implications for genetic inference. Evolution 60:1-12.